If you do indeed have a short circuit condition it will most likely be evident by measuring the +5vdc using dc volt function on your meter. Short circuits cause voltage regulators to go into protection mode and fold back their voltage.

More detailed testing can be done if you clearly state the type of arduino board you are using and how you are powering it.

If your MCU is short-circuited, it will be hot to the touch after you power on.

During normal operation, nothing on the MCU board (including the power regulator) should get hot. So if you use your finger to touch the components while powered on you should get a sense of whether there are any possible shorts.

This test however can not tell you whether an input pin is shorted since the current draw is very small and it wouldn't produce any heat or affect the supply voltage.